LOCUS       NZ_CP147585             5624 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain GN06667 plasmid unnamed1, complete sequence.
ACCESSION   NZ_CP147585
VERSION     NZ_CP147585.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123769
            Assembly: GCF_037280675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5624)
  AUTHORS   Parsons,J.B., Sidders,A.E., Velez,A.Z., Hanson,B.M.,
            Angeles-Solano,M., Ruffin,F., Rowe,S.E., Arias,C.A., Fowler,V.G.
            Jr., Thaden,J.T. and Conlon,B.P.
  TITLE     In-patient evolution of a high-persister Escherichia coli strain
            with reduced in vivo antibiotic susceptibility
  JOURNAL   Proc Natl Acad Sci U S A 121 (3), e2314514121 (2024)
   PUBMED   38190524
REFERENCE   2  (bases 1 to 5624)
  AUTHORS   Hanson,B.M., Parsons,J.B. and Conlon,B.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-FEB-2024) Center for Antimicrobial Resistance and
            Microbial Genomics, The University of Texas Health Sciences Center,
            1200 Pressler St, Houston, TX 77030, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: NOV-2021
            Assembly Method                   :: Flye v. v2.8.3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina NextSeq and Oxford Nanopore
            GridION X5
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037280675.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:09:56
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,102
            CDSs (total)                      :: 4,979
            Genes (coding)                    :: 4,766
            CDSs (with protein)               :: 4,766
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 213
            CDSs (without protein)            :: 213
            Pseudo Genes (ambiguous residues) :: 0 of 213
            Pseudo Genes (frameshifted)       :: 83 of 213
            Pseudo Genes (incomplete)         :: 136 of 213
            Pseudo Genes (internal stop)      :: 42 of 213
            Pseudo Genes (multiple problems)  :: 43 of 213
            Pseudo Genes (short protein)      :: 3 of 213
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147585.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5624
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GN06667"
                     /isolation_source="bloodstream"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed1"
                     /geo_loc_name="USA: Durham"
                     /lat_lon="36.0070 N 78.9371 W"
                     /collected_by="Duke Bloodstream Infection Biorepository"
     gene            1..1053
                     /locus_tag="WCU01_RS00005"
                     /old_locus_tag="WCU01_00005"
     CDS             1..1053
                     /locus_tag="WCU01_RS00005"
                     /old_locus_tag="WCU01_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_042011821.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPRGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            1055..1921
                     /locus_tag="WCU01_RS00010"
                     /old_locus_tag="WCU01_00010"
     CDS             1055..1921
                     /locus_tag="WCU01_RS00010"
                     /old_locus_tag="WCU01_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(3124..3315)
                     /locus_tag="WCU01_RS00015"
                     /old_locus_tag="WCU01_00015"
     CDS             complement(3124..3315)
                     /locus_tag="WCU01_RS00015"
                     /old_locus_tag="WCU01_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3379..3687
                     /locus_tag="WCU01_RS00020"
                     /old_locus_tag="WCU01_00020"
     CDS             3379..3687
                     /locus_tag="WCU01_RS00020"
                     /old_locus_tag="WCU01_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_040088330.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQG"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3903..>4334
                     /locus_tag="WCU01_RS00025"
                     /old_locus_tag="WCU01_00025"
                     /pseudo=""
     CDS             3903..>4334
                     /locus_tag="WCU01_RS00025"
                     /old_locus_tag="WCU01_00025"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4372..4903
                     /locus_tag="WCU01_RS00030"
                     /old_locus_tag="WCU01_00030"
                     /pseudo=""
     CDS             4372..4903
                     /locus_tag="WCU01_RS00030"
                     /old_locus_tag="WCU01_00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /name="MbeB family mobilization protein"
     gene            4910..5143
                     /locus_tag="WCU01_RS00035"
                     /old_locus_tag="WCU01_00035"
     CDS             4910..5143
                     /locus_tag="WCU01_RS00035"
                     /old_locus_tag="WCU01_00035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2949..3030
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          2305..2492
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          3347..3684
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.23"
                     /coverage="96.0"
                     /evalue="3.05e-66"
     Typing          3685..4499
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4505..5247
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.194"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgaatcttc aacaacgtat aaataaacta ccacaattat catccagttt ttcatttgga
       61 aaagatattg ataatattca ttcatttatc tttaacgaaa cttctaaaga taaaattgaa
      121 gatttactaa gaaaatgggt gtcaggcaat cagccctgtg tatttggtaa attggcaagc
      181 aagaaaatta aagggcttga tttccattta tctattgtaa atagccccca actatataat
      241 gatgatggtc atttgtttga ttttttgcgt aatgaaagag ttcgttttaa agaacgcgca
      301 agaagaggag aggtcagtgc gcatctcatt tattttattc atccacaact tgcctttgct
      361 cgtccatcag aagagttagt ggacatacaa aaatatattt gttcgctgca tatgccagag
      421 tgctatccaa taaaagagga tgttatttat actgaaagcg taccatttca ggataaagat
      481 gggctaaaaa tatataaggc tggtgttaat gttttttact cttctgctca tagaacaaga
      541 aatcatgata gaagaatacc aaggggaata cttatttctg taaatgcccc ggggcatttt
      601 atgaggctgg cgatagaaaa aggtttctat aaagatcaag aacaagcgtt agcggatatt
      661 cgtaacatga ctattcagtc tgttggtaag ggtgggtatt cacatccgga agggatttct
      721 acaacatggc attcagaatc taatttggat cgttttggat gcccagtgca caccggtaat
      781 agttcttatt acagcggttt ttatcatact gatgtattaa ttccaggaga attaactaag
      841 gatgaaagat tgctccatga aatagaaaat agtgatccaa tgatcttcaa ctggaatgta
      901 ttgttttatg tttcattaga agagtttcct atagatgatc cttattatgg agagtttatt
      961 ggtattcctg tagatgatgc atctatgttt tttaactcct ttcaaccaag gaaatttgaa
     1021 aacaaacccc tttatgagaa agaggatgat taatatgatt aaaggaatgc tttttgcttt
     1081 tttagcagcg ttctcatggg gggcagctat cgtaatgagc aaaaaaggag ttgaagaact
     1141 agatgccgga ggggtgtttt tctggcagat ttgtagtgca gtaatactat cttggatagt
     1201 tctttttata aaaagaaaaa aactcccatt aaactcaaaa gcgatacttg cttatgcgac
     1261 aggcgttttt gaaccattct tagcgtatac ttttacactc tacggacttt attttatttc
     1321 agcaggaagc gcatcaatta ttttttcact tgaatcagtg tttatattgg tgttatctgt
     1381 tcttatttgc tcagttaaaa ttaattcccc gcaatatttt atattgttcc ttataggtgc
     1441 aattgttggc agtattttgg tagccttgcc agacatcagt aatggatcga ataatattgt
     1501 tggatattgt cttgttgttg ccggtgtgtt atcggcagca ttttatgttg ttatatcgtc
     1561 tcgccttatt aaatcgtttg agcctatcac attattgagc ggacagttga cattctccct
     1621 tatactgtca tcgctcttta tttttatatc taaatcatca atttatcttc cgttggaatc
     1681 cgtgattatt gttttttcat ctggaatatt acaatatttt ttagcttttt gtttttactt
     1741 gaactccttg cgttggctcc cagttcattt ggcagggata atgttgtact ttattccgct
     1801 agttgcatta tttttgtcat ggttgttttt ggatgaacaa ttcacattct tacagggggt
     1861 aggatttatt gtaactgtgc taagtgtata ttttcttaac agaaaatact cagaggagta
     1921 acattctgtt caggattgcc ccccggcctc catcgatacc gtgccaaatg cacgtaaaaa
     1981 acgggagcgt ttctggtgtc ggaatgtaac caagggggtc agaggcgcgc taaaacgctc
     2041 tcaggggagt caaatagaga cgtttgtaac aaaaagatca aaggatcctc ttgagatcct
     2101 ttttttctgc gcgtaatctg ctgcctgtaa acgaaaaaac cgccttgcag ggcggtttga
     2161 tcgaaggtta agtcagcttg cagactgctt aaccaggtaa ctgtcttatg cgagacgagt
     2221 caccaaaatt gttcttctag tgtagccgca ctccggcagc cacttcaagt actctctaaa
     2281 tatctcgcac atgactttta ccaatggctg ctgccagtgg cgctttgtgg tgtcttttcc
     2341 gggttggacc caagagaaca gttaccggag aaggcgcagc agtcgggctg aacggggggt
     2401 tcctgcatac agcccagccc ggagcgaact gcctaagtcg ccccgagata ccagaagacg
     2461 tgagctatga gaaagcgcca cgtgtcccgt aagggagaaa ggcggaaaag gtatccggta
     2521 atcgatatgg cgggaacgtg ggggcgcagg agggagcgat tcaccggaaa cggtgatgat
     2581 ctttaagcca cgtcgggttt cgccaccgct ggcggatttc atggttgagc cgcaaggctc
     2641 ccacagatgc accgaaaaag tgtctgtttt gtgaagtccg tcaggggggc ggagcctatg
     2701 gaaaaagcgc ctccggcgcg gcctttcccg gggtttcgtt ttttgcgcac atgttctttc
     2761 ctggtttatc cccgggttct gtggataaca gggttagcgt ttttgagaaa ggagagtccg
     2821 ctcgccgcag ccgaacgacc gagcgtagcg agtcagtgag cgaggaagcg gaagagcgcc
     2881 tgaactggca ttttctcctt acgcatctgt gcggcatttc acaccggaca tggcgcactt
     2941 ttcatacaat ccgcactgat gccgaatggt taagccagta tacactccgc tatcgctacg
     3001 tgactgggtc agggcttcgc cccgacaccc caaaggtcaa cggcctgacg cgccctggcg
     3061 ggcttgtctg ctcccggcat ccgctcacag acaagctgtg accgtctccg ggagctgcat
     3121 gtgtcagcgg ttttcaccgt catccccgaa gcgtgcgagg caactgcggt aaagctcatc
     3181 ggcgtggtcg tgaagcgatt cacagatgtc tgcctgttca tccgcgtcca gttcgttgag
     3241 cttctccagc agcgttaatg tctggcctct gatgaagcgg gccatgttaa gggcggtttt
     3301 ttcctgtttg gtcactgatg cctccgtgta aggggggttc tgttcatggg ggtaatgata
     3361 ccgatgaaac gcgagaggat gctcacgata cgggttactg atgatgaaca tgcccggtta
     3421 ctggaacgct gtgagggtaa acaactggcg gtatggatgc ggcgggtctg cctgggtgag
     3481 ccggttgccc gttccgggaa gctgccgaca ctggcaccgc cgttactgcg tcagctggcc
     3541 gccatcggga ataaccttaa ccagacagcg aggaaggtga acagcgggca gtggtcttcc
     3601 ggtgaccggg ttcaggtggt ggccgcactg atggccatcg gggatgagct gcgccggctg
     3661 cgtctggcgg tcagggaaca gggatgatag ttaagtttca tgccagggga aaaggtggtg
     3721 gcagtggtcc ggttgattac ctgctgggaa gggagcgtaa ccgggaaggg gcaacggtgc
     3781 ttcaggggaa tccggaagag gtccgggaac tcatcgatgc cacgccattt gcgaagaaat
     3841 acacgtcagg tgttctgtcg ttcgcggaga aggagctgcc gcctggaggg cgtgaaaaag
     3901 tgatggcgag ctttgagcgt gtactgatgc ccggtctcga gaaaaatcag tacagcatcc
     3961 tgtgggtgga gcaccaggac aagggacggc ttgagctgaa ttttgtcatt ccgaacatgg
     4021 agctacagac cggaaaacgc ctccagccgt actacgaccg ggcagacagg ccgagaattg
     4081 atgcctggca gacgctggtg aatcaccatt acggtctgca tgaccccaac gccccggaga
     4141 accgccggac gctgaccctt cctgataacc tgccggaaac gaaacaggcg cttgctgagg
     4201 gcgtcacacg cgggatagac gcgctttacc atgccggaga gataaaaggc cgtcaggatg
     4261 tgattcaggc gctcacagag gcggggcttg aagtggtcag ggtgacgcga agcagtatca
     4321 gcattgcaga cccgaacggc gggaggaata tcagactgaa aggagcgttt tatgagcaat
     4381 cttttacaga cgggcgcgga gttcgagaaa aagctgaaag agagagccga atctacagag
     4441 aaaatgctga acgacgagtt caggaagctc gaagaatctg taaacaggga actgacctca
     4501 taacgaatct ttaatcagga acgctatcaa cgaccataca acagccctga aagaactgct
     4561 ggagaggtat cagaaaacga ccgtcgatac gatggacgcg cactggaaaa ccgtactgaa
     4621 aatgagcgtg aaacgctggc tgtggctgat tatcgtctca gtactgatgt ttgccacgac
     4681 cgggagtctg ctgtggtacc agggcatgaa gataaacgcg aatatgaata ttctccgcga
     4741 gcagaaagag agtctggaga agctgaacgc gaagacatgg ggcgtgcgtt atcacgagga
     4801 cagcaacgga cgttttctag tgttgccgaa ggggatgaaa gccgaaacga actggacgaa
     4861 ggacaacggc aaactgaacg cagtgagact ggtgcaggag tgacagagca tgacggagct
     4921 ggaaagacat ttgctgaacg cattagagca actgcaacag gactatatgc agcggctgaa
     4981 cgaatgggag aacgccttcg tggaattgca gaaaatgttt tcgcttacgc aacgggacaa
     5041 cgcgatgctg aacgggcgag tcatgcagtt gagtcagcag gtgcagcact tgagcgagcg
     5101 gacagaacgc ttgagccagt tatacagcga gaacaggaga taagggatga acggctgatg
     5161 caggaacgcg aacatgagtt atctctggag cgggagcgtc agccggaaat ccaggagcgg
     5221 acactgggtg gcccttcgct gggatggtga aaccatgaaa aatgacgtgt tcagtggatt
     5281 aaggcgggct aatgtggcct gtagcatctg gttgcatagg tattcatgcg gttaaaattt
     5341 atcaggtgcg atcgcggcag tttttcgggt ggtttgttgc catttttacc tgtctgctgc
     5401 cgtgatcgca ccgaacgcgt tttggcggtg cgtacaatgc gacgttatgg taaatggagc
     5461 ggattttcag gaaggagtga tactaacaac tcgaacactg tgcaaataat gattttttta
     5521 aaatatcggt aacgataata aattatttcg ttttacgccg gtaataaata taatgtagtt
     5581 tcagtatata aaaaaaatat atgaggtgtc ttgtgggagc tttc
//
